[gmx-users] Decane layer

[M.Naser]

Thanks again david.

Is there any way I can insert protein in a water box instead of other way
around. I tired with genbox with -ci  and did not work with me.

With regards,

Abu

> On Fri, 2005-08-05 at 15:40 +0100, M.Naser wrote:
>> Thnaks david.
>>
>> Can you give me some idea of how long it suppose to take?
> unless the conformation is really bad a few hundred steps should
> suffice. then you should run with pressure coupling.
>
> if all else fails you can make the box bigger using editconf and run
> with pressure coupling to have it contract again.
>>
>>
>>
>>
>>
>> > On Fri, 2005-08-05 at 15:19 +0100, M.Naser wrote:
>> >> Hi All,
>> >>
>> >> I have a decane box with 730 kg/m^3 and trying to run trial
>> simulation
>> >> but
>> >> crashing on me. It might be due to the bad contact. Is there any way
>> I
>> >> can
>> >> avoid that?
>> >
>> > long energy minimization
>> >
>> >>
>> >> My mdp file as follows:
>> >>
>> >> title		    =  Decane
>> >> cpp                 =  /lib/cpp
>> >> ;define              =  -DPOSRES ;  -DFLEX_SPC  -DFLEXIBLE
>> >> ;include             =  -I/home/bio/mn2/tutor/project1/
>> >>
>> >> integrator          = md
>> >> dt                  = 0.001
>> >> nsteps              = 1000000
>> >> tint		    = 0
>> >> init_step           = 0
>> >> comm_mode           = linear
>> >> nstcomm             = 1
>> >>
>> >>
>> >>
>> >>
>> >> nstlist             = 10
>> >> ns_type 	    = grid
>> >> pbc                 = xyz
>> >> rlist		    = 0.9
>> >>
>> >>
>> >>
>> >>
>> >> coulombtype	    = PME
>> >> rcoulomb-switch     = 0
>> >> rcoulomb            = 0.9
>> >> vdwtype		    = switch
>> >> rvdw-switch	    = 0.8
>> >> rvdw                = 0.9
>> >> fourierspacing     = 0.1
>> >> pme_order          = 4
>> >> ewald_rtol          =1e-5
>> >> ewald_geometry      =3dc
>> >> surface_epsilon     =0
>> >> optimize_fft        =yes
>> >> DispCorr            = no
>> >> table-extension     = 1
>> >>
>> >> Tcoupl              =  Berendsen
>> >> tc_grps	            = system
>> >> tau_t               =  0.1
>> >> ref_t		    =  300
>> >>
>> >> Pcoupl              = no
>> >>
>> >> constraints               = all-bonds
>> >> constraint_algorithm      = shake ;lincs
>> >> unconstrained_start       = no
>> >> shake_tol                 = 0.0001
>> >>
>> >>
>> >> nstxout            = 1000
>> >> nstvout            = 1000
>> >> nstfout            = 0
>> >> nstlog            =  1000
>> >> nstenergy         =  1000
>> >> nstxtcout         =  1000
>> >> xtc_precision     = 1000
>> >>
>> >> Thanks in advance,
>> >>
>> >> Abu
>> >>
>> >>
>> >>
>> >>
>> >>
>> >> __________________________________________________________________
>> >>
>> >> DISCLAIMER:
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>> > --
>> > David.
>> > ________________________________________________________________________
>> > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
>> > Dept. of Cell and Molecular Biology, Uppsala University.
>> > Husargatan 3, Box 596,          75124 Uppsala, Sweden
>> > phone:  46 18 471 4205          fax: 46 18 511 755
>> > spoel at xray.bmc.uu.se    spoel at gromacs.org
>> http://xray.bmc.uu.se/~spoel
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> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,          75124 Uppsala, Sweden
> phone:  46 18 471 4205          fax: 46 18 511 755
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
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